dockerfile updates

Author: Jon Palmer

Dockerfile

@@ -7,18 +7,22 @@ COPY gm_key_64.gz /home/linuxbrew/gm_key_64.gz
 COPY signalp-4.1c.Linux.tar.Z /home/linuxbrew/signalp-4.1c.Linux.tar.Z
 
 RUN tar zxvf gm_et_linux_64.tar.gz && \
-    mv /home/linuxbrew/gm_et_linux_64/gmes_petap $GENEMARK_PATH && \
     gunzip gm_key_64.gz && \
     cp gm_key_64 /home/linuxbrew/.gm_key && \
-    rm -rf /home/linuxbrew/gm_et_linux_64 gm_key_64 gm_et_linux_64.tar.gz
+    rm -rf gm_et_linux_64.tar.gz
 
 RUN zcat signalp-4.1c.Linux.tar.Z | tar -xvf - && \
-    sed -i 's,/usr/cbs/bio/src/signalp-4.1,/home/linuxbrew/data/signalp-4.1,g' signalp-4.1/signalp && \
-    mv /home/linuxbrew/signalp-4.1 /home/linuxbrew/data/signalp-4.1 
+    sed -i 's,/usr/cbs/bio/src/signalp-4.1,/home/linuxbrew/signalp-4.1,g' signalp-4.1/signalp
 
 COPY RepBaseRepeatMaskerEdition-20170127.tar.gz /home/linuxbrew/RepBaseRepeatMaskerEdition-20170127.tar.gz
 
 RUN tar zxvf RepBaseRepeatMaskerEdition-20170127.tar.gz -C /home/linuxbrew/.linuxbrew/opt/repeatmasker/libexec
 RUN brew postinstall repeatmasker
 
-RUN funannotate setup -m dep -d /home/linuxbrew/DB
+ENV PATH=/home/linuxbrew/gm_et_linux_64/gmes_petap:/home/linuxbrew/signalp-4.1:/home/linuxbrew/.linuxbrew/opt/braker/libexec:$PATH
+
+RUN funannotate setup -m dep -d /home/linuxbrew/DB
+
+RUN funannotate eggnog --install fuNOG
+
+WORKDIR /home/linuxbrew/data

Dockerfile-base

@@ -18,7 +18,7 @@ RUN git clone https://github.com/Linuxbrew/brew.git /home/linuxbrew/.linuxbrew \
 
 USER linuxbrew
 WORKDIR /home/linuxbrew
-ENV PATH=/home/linuxbrew/funannotate:/home/linuxbrew/conda/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/linuxbrew/augustus/bin:/home/linuxbrew/.linuxbrew/opt/repeatmasker/libexec/util:/home/linuxbrew/data/gm_et_linux_64/gmes_petap:/home/linuxbrew/data/signalp-4.1:$PATH \
+ENV PATH=/home/linuxbrew/funannotate:/home/linuxbrew/conda/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/home/linuxbrew/augustus/bin:/home/linuxbrew/.linuxbrew/opt/repeatmasker/libexec/util:/home/linuxbrew/gm_et_linux_64/gmes_petap:/home/linuxbrew/signalp-4.1:$PATH \
 	SHELL=/bin/bash
 
 RUN brew doctor || true
@@ -65,10 +65,7 @@ RUN wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-03-17.tar.gz && \
 RUN rm /home/linuxbrew/.linuxbrew/bin/tblastn
 
 #grab most recent version of funannotate
-RUN git clone git://github.com/nextgenusfs/funannotate.git && \
-    cd funannotate && \
-    git checkout tags/0.6.1 && \
-    cd ..
+RUN git clone git://github.com/nextgenusfs/funannotate.git
 
 ENV AUGUSTUS_CONFIG_PATH=/home/linuxbrew/augustus/config \
     EVM_HOME=/home/linuxbrew/.linuxbrew/opt/evidencemodeler \